neurodash 0.0.1__tar.gz

neurodash-0.0.1/LICENSE

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neurodash-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: neurodash
+Version: 0.0.1
+Summary: Web dashboard neurobehavioral data explorer.
+Author: EricThomson
+Author-email: EricThomson <thomson.eric@gmail.com>
+License-Expression: Apache-2.0
+License-File: LICENSE
+Requires-Dist: dash
+Requires-Dist: plotly
+Requires-Dist: neo
+Requires-Dist: quantities
+Requires-Dist: lspopt
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: pandas
+Requires-Dist: openpyxl
+Requires-Dist: imageio[ffmpeg,pyav]
+Requires-Dist: pyqt6
+Requires-Dist: pyqtgraph
+Requires-Python: >=3.12
+Project-URL: Repository, https://github.com/EricThomson/neurodash
+Description-Content-Type: text/markdown
+
+# neurodash
+<img src="https://raw.githubusercontent.com/EricThomson/neurodash/main/src/neurodash/assets/logo/neurodash_logo_trimmed.png" alt="neurodash logo" align="right" width="250">
+Lightweight dashboard for exploratory analysis of neurobehavioral data.
+
+## Setting up and running
+Make sure uv is installed.
+
+    uv sync
+    source .venv/Scripts/activate
+
+Run with `python app.py` and explore away! Assumes you have neural data in plexon, and behavioral data in Excel. 
+
+## To do
+- export csv/png
+- docs
+  - basic how to use
+  - explain back-end stuff like channels/streaming neo/plx
+- Testing, linting, etc
+  

neurodash-0.0.1/README.md

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+# neurodash
+<img src="https://raw.githubusercontent.com/EricThomson/neurodash/main/src/neurodash/assets/logo/neurodash_logo_trimmed.png" alt="neurodash logo" align="right" width="250">
+Lightweight dashboard for exploratory analysis of neurobehavioral data.
+
+## Setting up and running
+Make sure uv is installed.
+
+    uv sync
+    source .venv/Scripts/activate
+
+Run with `python app.py` and explore away! Assumes you have neural data in plexon, and behavioral data in Excel. 
+
+## To do
+- export csv/png
+- docs
+  - basic how to use
+  - explain back-end stuff like channels/streaming neo/plx
+- Testing, linting, etc
+  

neurodash-0.0.1/pyproject.toml

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+[build-system]
+requires = ["uv_build>=0.11.26,<0.12.0"]
+build-backend = "uv_build"
+
+[project]
+name = "neurodash"
+version = "0.0.1"
+description = "Web dashboard neurobehavioral data explorer."
+readme = "README.md"
+requires-python = ">=3.12"
+license = "Apache-2.0"
+license-files = ["LICENSE"]
+authors = [
+    { name = "EricThomson", email = "thomson.eric@gmail.com" }
+]
+dependencies = [
+  # Core UI
+  "dash",
+  "plotly",
+  # Neural I/O
+  "neo",
+  "quantities",
+  # Signal processing
+  "lspopt",
+  "numpy",
+  "scipy",
+  # Behavioral I/O
+  "pandas",
+  "openpyxl",
+  # Video I/O (pyqtdash)
+  "imageio[ffmpeg,pyav]",
+  # pyqtdash viewer
+  "pyqt6",
+  "pyqtgraph",
+]
+
+[project.urls]
+Repository = "https://github.com/EricThomson/neurodash"
+
+[tool.uv.build-backend]
+module-root = "src"

neurodash-0.0.1/src/neurodash/behavior_io.py

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+"""
+behavior_io.py — EthoVision behavioral data loading for neurodash.
+
+Loads EthoVision Excel exports and provides position/motion extraction
+and neural sync utilities.
+
+EthoVision Excel format:
+  - Row 0: header row count (n_header)
+  - Rows 1..n_header-3: key/value metadata pairs
+  - Row n_header-2: column names
+  - Row n_header-1: units
+  - Row n_header onward: tracking data (~30 Hz)
+
+Key columns: Recording time, X/Y center/nose/tail (cm), Velocity (cm/s),
+Direction (deg), Distance moved (cm).
+"""
+
+import re
+from pathlib import Path
+
+import numpy as np
+import pandas as pd
+
+
+# ---------------------------------------------------------------------------
+# Loading
+# ---------------------------------------------------------------------------
+
+def load_behavior_file(path):
+    """Load an EthoVision Excel export.
+
+    Parameters
+    ----------
+    path : str or Path
+
+    Returns
+    -------
+    metadata : dict
+        Key/value pairs from the header block.
+    data : pd.DataFrame
+        Tracking data, one row per frame. All numeric where possible;
+        non-numeric EthoVision markers become np.nan.
+        data.attrs['units'] holds a {column: unit_string} dict.
+    """
+    raw = pd.read_excel(path, header=None)
+    n_header = int(raw.iloc[0, 1])
+
+    metadata = {}
+    for i in range(1, n_header - 2):
+        key = str(raw.iloc[i, 0]).strip()
+        val = raw.iloc[i, 1]
+        if key and key != 'nan':
+            metadata[key] = val if not _is_blank(val) else None
+
+    col_names = raw.iloc[n_header - 2].tolist()
+    units = raw.iloc[n_header - 1].tolist()
+
+    data = raw.iloc[n_header:].copy()
+    data.columns = col_names
+    data = data.reset_index(drop=True)
+    data.attrs['units'] = {col: str(u) for col, u in zip(col_names, units)}
+
+    for col in data.columns:
+        data[col] = pd.to_numeric(data[col], errors='coerce')
+
+    return metadata, data
+
+
+def _is_blank(val):
+    if val is None:
+        return True
+    try:
+        return pd.isna(val)
+    except (TypeError, ValueError):
+        return str(val).strip() == ''
+
+
+# ---------------------------------------------------------------------------
+# Metadata helpers
+# ---------------------------------------------------------------------------
+
+def get_recording_delay(metadata):
+    """Parse 'Recording after' delay from EthoVision metadata.
+
+    Returns the number of seconds between trial start and when video
+    recording began. Used to compute frame_offset = round(delay * fps).
+
+    Parameters
+    ----------
+    metadata : dict
+        Output of load_behavior_file.
+
+    Returns
+    -------
+    delay_seconds : float
+    """
+    recording_after = str(metadata.get('Recording after', '+ 00:00:00.000'))
+    time_part = recording_after.strip().lstrip('+ ').strip()
+    h, m, s = time_part.split(':')
+    return int(h) * 3600 + int(m) * 60 + float(s)
+
+
+def get_display_metadata(metadata):
+    """Extract the subset of metadata fields useful for sidebar display.
+
+    Parameters
+    ----------
+    metadata : dict
+        Output of load_behavior_file.
+
+    Returns
+    -------
+    dict with keys:
+        mouse_id, experiment, trial_name, start_time, recording_duration,
+        arena_name, arena_id, video_stem,
+        missed_samples_pct, subject_not_found_pct, interpolated_pct
+    """
+    def _duration_str(val):
+        """Strip leading '+ ' from EthoVision duration strings."""
+        if val is None:
+            return None
+        return str(val).strip().lstrip('+ ').strip()
+
+    def _pct_float(val):
+        """Parse '0.0 %' → 0.0."""
+        if val is None:
+            return None
+        m = re.search(r'[\d.]+', str(val))
+        return float(m.group()) if m else None
+
+    video_path = metadata.get('Video file')
+    video_filename = Path(video_path).name if video_path else None
+
+    return {
+        'mouse_id':              metadata.get('mouse ID'),
+        'experiment':            metadata.get('Experiment'),
+        'trial_name':            metadata.get('Trial name'),
+        'start_time':            metadata.get('Start time'),
+        'recording_duration':    _duration_str(metadata.get('Recording duration')),
+        'arena_name':            metadata.get('Arena name'),
+        'arena_id':              metadata.get('Arena ID'),
+        'video_filename':        video_filename,
+        'missed_samples_pct':    _pct_float(metadata.get('Missed samples')),
+        'subject_not_found_pct': _pct_float(metadata.get('Subject not found')),
+        'interpolated_pct':      _pct_float(metadata.get('Interpolated samples')),
+    }
+
+
+# ---------------------------------------------------------------------------
+# Position
+# ---------------------------------------------------------------------------
+
+def extract_position(data, point='center'):
+    """Extract x/y position time series for a tracked body point.
+
+    Parameters
+    ----------
+    data : pd.DataFrame
+        Output of load_behavior_file.
+    point : {'center', 'nose', 'tail'}
+
+    Returns
+    -------
+    t : np.ndarray — Recording time (s)
+    x : np.ndarray — X position (cm)
+    y : np.ndarray — Y position (cm)
+    """
+    point_map = {
+        'center': ('X center', 'Y center'),
+        'nose':   ('X nose',   'Y nose'),
+        'tail':   ('X tail',   'Y tail'),
+    }
+    if point not in point_map:
+        raise ValueError(f"point must be one of {list(point_map)}, got '{point}'")
+    x_col, y_col = point_map[point]
+    t = data['Recording time'].to_numpy(dtype=float)
+    x = data[x_col].to_numpy(dtype=float)
+    y = data[y_col].to_numpy(dtype=float)
+    return t, x, y
+
+
+def estimate_position_pixels(x, y, video_width, video_height,
+                             scale_x=1.0, scale_y=1.0,
+                             offset_x=0.0, offset_y=0.0,
+                             padding=0.1):
+    """Map EthoVision cm coordinates to video pixel coordinates.
+
+    Uses data bounds + padding as a proxy for arena extent (uncalibrated).
+    Pass scale_x/y, offset_x/y from a saved arena calibration to refine.
+
+    Y is flipped: EthoVision Y increases upward, image Y increases downward.
+
+    Parameters
+    ----------
+    x, y : np.ndarray — position in cm
+    video_width, video_height : int — frame dimensions in pixels
+    scale_x, scale_y : float — calibration scale factors
+    offset_x, offset_y : float — calibration pixel offsets
+    padding : float — fractional padding around data bounds
+
+    Returns
+    -------
+    px, py : np.ndarray — pixel coordinates
+    """
+    x_min, x_max = np.nanmin(x), np.nanmax(x)
+    y_min, y_max = np.nanmin(y), np.nanmax(y)
+    x_pad = (x_max - x_min) * padding
+    y_pad = (y_max - y_min) * padding
+    x_min -= x_pad; x_max += x_pad
+    y_min -= y_pad; y_max += y_pad
+
+    px = ((x - x_min) / (x_max - x_min) * video_width) * scale_x + offset_x
+    py = ((1.0 - (y - y_min) / (y_max - y_min)) * video_height) * scale_y + offset_y
+    return px, py
+
+
+# ---------------------------------------------------------------------------
+# Motion
+# ---------------------------------------------------------------------------
+
+def compute_motion(data, point='center'):
+    """Compute frame-to-frame displacement and speed from tracked position.
+
+    Re-derives from x/y coordinates rather than EthoVision's 'Distance moved'
+    column, so the calculation is transparent and reproducible.
+
+    Returns
+    -------
+    t : np.ndarray — Recording time (s)
+    displacement : np.ndarray — distance moved since previous frame (cm); first value NaN
+    speed : np.ndarray — instantaneous speed (cm/s); first value NaN
+    """
+    t, x, y = extract_position(data, point=point)
+    dx = np.diff(x)
+    dy = np.diff(y)
+    dt = np.diff(t)
+    displacement = np.sqrt(dx**2 + dy**2)
+    speed = displacement / dt
+    displacement = np.concatenate([[np.nan], displacement])
+    speed = np.concatenate([[np.nan], speed])
+    return t, displacement, speed
+
+
+# ---------------------------------------------------------------------------
+# Neural sync
+# ---------------------------------------------------------------------------
+
+def get_recording_delay_from_data(data):
+    """Return the offset between trial start and behavioral t=0.
+
+    Alias for get_recording_delay that works directly from the data DataFrame
+    when metadata is not available separately.
+    """
+    # Recording time in the DataFrame starts at 0 when video recording began.
+    # The delay relative to trial start is already baked into the time axis.
+    return float(data['Recording time'].iloc[0])
+
+
+def sync_to_neural(data, neural_t_offset=0.0):
+    """Align behavioral Recording time to a shared neural time axis.
+
+    Parameters
+    ----------
+    data : pd.DataFrame
+    neural_t_offset : float
+        Seconds to add to behavioral Recording time to align with neural time.
+
+    Returns
+    -------
+    t_neural : np.ndarray
+    """
+    t_behavior = data['Recording time'].to_numpy(dtype=float)
+    return t_behavior + neural_t_offset
+
+
+def get_behavior_at_neural_times(data, query_times, column, neural_t_offset=0.0):
+    """Interpolate a behavioral variable onto arbitrary neural timepoints.
+
+    Parameters
+    ----------
+    data : pd.DataFrame
+    query_times : array-like — neural timepoints (s)
+    column : str — column name (e.g. 'Velocity', 'X center')
+    neural_t_offset : float
+
+    Returns
+    -------
+    values : np.ndarray — interpolated values; NaN outside behavioral range
+    """
+    t_neural = sync_to_neural(data, neural_t_offset=neural_t_offset)
+    values = data[column].to_numpy(dtype=float)
+    query_times = np.asarray(query_times, dtype=float)
+    return np.interp(query_times, t_neural, values, left=np.nan, right=np.nan)